Hyperlink management system
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Help Index

1. About Hyperlink Management System
2. How to create hyperlinks using the system
3. All database search
4. ID converter system
5. Downloading ID tables
6. ID Resolver
7. Web Service
8. Collected databases/IDs
9. Release history

1. About Hyperlink Management System

Hyperlink Management System is a system for automatically updating and maintaining hyperlinks among major public databases in the field of life science. Everyday, we create corresponding tables of data IDs that are used in major databases for genes and proteins, and provide a cgi-program that returns correct and up-to-date URLs of corresponding data in many databases. By using the CGI program on this server, users can easily create hyperlinks to major databases in their own databases and homepages. Furthermore, on this web site, we provide useful tools such as "All Database Search", "ID converter system", and "Downloading ID tables".
This System was developed at the Biological Information Research Center of the National Institute of Advanced Industrial Science and Technology (AIST) with the financial support from the JST (2006-2008). Since 2008, the system is developed at the Biomedicinal Information Research Center of AIST with a support from the Integrated Database Project of the Ministry of Economy, Trade and Industry of Japan (a portal for the project: MEDALS).

Creative Commons License
This work is licensed under a Creative Commons Attribution 2.1 Japan License.
Please cite the paper below if you utilize the systems provided on this web site.
Imanishi T and Nakaoka H (2009) Hyperlink Management System and ID Converter System: enabling maintenance-free hyperlinks among major biological databases. Nucleic Acids Research 37(Web Server Issue) doi:10.1093/nar/gkp355. (http://biodb.jp/)

2. How to create hyperlinks using the system

(1) A simple method

In order to create hyperlinks using the CGI-program of the Hyperlink Management System, use the following URL as a target URL.. 
			http://biodb.jp/hfs.cgi?id=[ID]&type=[ID Type]&db=[Database Name]
The parameters given to the CGI-program are as follows.

  1. [ID]
    Source ID (original ID).

  2. [ID Type]
    The type of source ID. Choose from below.
    ID list

  3. [Database name]
    The name of target database. Choose from below.
    Database list

Sample
The hyperlink to the "Transcript view" of H-InvDB using the INSD accession number "BC053657" will be the following URL. 
		http://biodb.jp/hfs.cgi?id=BC053657&type=ACC_ID&db=TRANSCRIPTVIEW

In HTML, you can write as follows. 
		<a href='http://biodb.jp/hfs.cgi?id=BC053657&type=ACC_ID&db=TRANSCRIPTVIEW'>BC053657</a>
		Sample：BC053657

ID list for human
No.FormatOutline
1ACC_IDAccession Number
2HIT_IDH-Inv transcript ID (HIT)
3HIX_IDH-Inv cluster ID (HIX)
4HIP_IDH-Inv protein ID (HIP)
5UNIPROT_IDUniProt Accession Number
6GENE_SYMBOLHUGO gene symbol
7REF_SEQRefSeq
8OMIM_IDOMIM ID
9GENE_IDGeneID
10PUBMED_IDPubMed ID
11JSNP_IDdbSNP rs#
12MS_IDMarker Name
13PDB_IDPDB ID
14FR_IDfRNAdb ID
15ENST_IDEnsembl Transcript ID
16ENSG_IDEnsembl Gene ID
17CLONE_IDClone ID (by NBRC)
18FLJ_IDFLJ ID (by NBRC)
19HPRD_IDHPRD ID
20CIPRO_IDCIPRO ID
21KEGG_IDKEGG Gene ID
22PATHWAY_IDKEGG Pathway ID
23CCO_PDBECHEM_IDPdbeChem ID
24CCO_DRUGBANK_IDDrugBank ID



ID list for mouse
No.FormatOutline
1MMU_MGI_IDMGI Marker Accession ID
2MMU_ACC_IDAccession Number
3HIT_IDH-Inv transcript ID (HIT)
4MMU_UNIPROT_IDUniProt Accession Number
5MMU_REF_SEQRefSeq
6MMU_GENE_IDGeneID
7MMU_PUBMED_IDPubMed ID
8MMU_ENST_IDEnsembl Transcript ID
9MMU_ENSG_IDEnsembl Gene ID
10MMU_CLONE_IDClone ID(FANTOM)
11MMU_GENE_SYMBOLMouse Gene Symbol(MGI)
12MMU_PDB_IDPDB ID
13MMU_BRC_MS_IDBRC ID
14MMU_ALLELE_IDALLELE ID
15MMU_KEGG_IDKEGG Gene ID
16MMU_PATHWAY_IDKEGG Pathway ID



ID list for rattus
No.FormatOutline
1RNO_ACC_IDAccession Number
2HIT_IDH-Inv transcript ID (HIT)
3RNO_REF_SEQRefSeq
4RNO_GENE_IDGeneID
5RNO_PUBMED_IDPubMed ID
6RNO_UNIPROT_IDUniProt Accession Number
7RNO_ENST_IDEnsembl Transcript ID
8RNO_ENSG_IDEnsembl Gene ID
9RNO_RGD_IDRGD ID
10RNO_KEGG_IDKEGG Gene ID
11RNO_PATHWAY_IDKEGG Pathway ID



ID list for Ciona intestinalis
No.FormatOutline
1CIN_ACC_IDAccession Number
2HIT_IDH-Inv transcript ID (HIT)
3CIN_UNIPROT_IDUniProt Accession Number
4CIN_UNIREF_IDUniRef100 Accession Number
5CIN_REF_SEQRefSeq
6CIN_GENE_IDGeneID
7CIN_PUBMED_IDPubMed ID
8CIN_ENST_IDEnsembl Transcript ID
9CIN_ENSG_IDEnsembl Gene ID
10CIN_CIPRO_IDCipro ID
11CIN_GHOST_IDGhost ID
12CIN_ANISEED_IDAniseed Gene ID



ID list for Chemical compounds
No.FormatOutline
1CCO_CHEBI_IDChEBI ID
2CCO_DRUGBANK_IDDrugBank ID
3CCO_KEGGCOMPOUND_IDKEGG Compound ID
4CCO_KEGGDRUG_IDKEGG Drug ID
5CCO_NIKKAJI_IDNIKKAJI ID
6CCO_PDBECHEM_IDPDBeChem ID
7CCO_PHARMGKB_IDPharmGKB ID
8CCO_C_IDPubChem Compound ID
9CCO_S_IDPubChem Substance ID
10PDB_IDPDB ID
11CCO_PUBMED_IDPubMed ID
12UNIPROT_IDUniprot Accession Number
13CCO_CAS_IDCAS ID *1
14CCO_KNAPSACK_IDKNApSAcK ID
15CCO_HMDB_IDHMDB Accession Number
*1 CAS Registry Number is a Registered Trademark of the American Chemical Society.


Database list for human
No.FormatOutline
1TRANSCRIPTVIEWH-InvDB (Transcript view)
2LOCUSVIEWH-InvDB (Locus view)
3GINTEGRAH-InvDB (G-integra)
4PPIH-InvDB (PPI view)
5NUCLEOTIDENucleotide (NCBI)
6GENBANKGenBank (NCBI)
7ENTREZGENEEntrez Gene (NCBI)
8OMIMOMIM (NCBI)
9PUBMEDPubMed (NCBI)
10GEMDBJGeMDBJ
11HUGOHUGO
12MUTATIONVIEWMutationView
13HGOLDH-GOLD
14PDBPDB
15UNIPROTUniProt
16ENSTEnsembl Transcriptview
17ENSGEnsembl Geneview
18GGDBGGDB
19FRNADBfRNAdb
20NBRCNBRC
21HGPDHGPD
22KEGGKEGG Gene
23PATHWAYKEGG Pathway
24HPRDHPRD
25LEGENDALEGENDA
26EVOLAEVOLA
27HDBASH-DBAS
28GCOMPASSG-Compass
29PROTEINVIEWProtein View
30CIPROCIPRO
31HANGELH-ANGEL
32FLJHFLJ Human cDNA
33VARYSYSDBVarySysDB
34PDBECHEMPDBeChem
35DRUGBANK_HDrugBank
36WIKIPEDIA_HPWikipedia Human proteins
37JSNPJSNP



Database list for mouse
No.FormatOutline
1NUCLEOTIDENucleotide (NCBI)
2GENBANKGenBank (NCBI)
3ENTREZGENEEntrez Gene (NCBI)
4PUBMEDPubMed (NCBI)
5UNIPROTUniProt
6ENSTEnsembl Transcriptview
7ENSGEnsembl Geneview
8KEGGKEGG Gene
9PATHWAYKEGG Pathway
10EVOLAEVOLA
11MGIMGI Gene
12IKMCIKMC
13FANTOMFANTOM
14PDBPDB
15BRC_MSBRC Mouse Strain
16ALLELEMGI Allele
17SYMBOLMouse Gene Symbol



Database list for rattus
No.FormatOutline
1NUCLEOTIDENucleotide (NCBI)
2GENBANKGenBank (NCBI)
3ENTREZGENEEntrez Gene (NCBI)
4PUBMEDPubMed (NCBI)
5UNIPROTUniProt
6ENSTEnsembl Transcriptview
7ENSGEnsembl Geneview
8KEGGKEGG Gene
9PATHWAYKEGG Pathway
10EVOLAEVOLA
11RGDRat Genome Database



Database list for Ciona intestinalis
No.FormatOutline
1NUCLEOTIDENucleotide (NCBI)
2GENBANKGenBank (NCBI)
3ENTREZGENEEntrez Gene (NCBI)
4PUBMEDPubMed (NCBI)
5UNIPROTUniProt
6UNIREFUniRef100
7ENSTEnsembl Transcriptview
8ENSGEnsembl Geneview
9CIPROCipro
10TRANSCRIPTVIEWH-InvDB (Transcript view)
11GHOSTGhost
12ANISEEDAniseed



Database list for Chemical compounds
No.FormatOutline
1PUBCHEM_CPubChem Compound
2PUBCHEM_SPubChem Substance
3DRUGBANKDrugBank
4KEGGDRUGKegg Drug
5KEGGCOMPOUNDKegg Compound
6CHEBIChEBI
7PHARMGKBPharmGKB
8PDBECHEMPDBeCem
9NIKKAJINIKKAJI
10CASCAS
11CITEXPLORECiteXplore
12PUBMEDPubMed (NCBI)
13PDBJPDBj
14UNIPROTUniProt
15KNAPSACKKNApSAcK
16HMDBHMDB
17JECDBJECDB



(2) Using Real-Time Link Generator

By a web-service connection to the Real-Time Link Generator of Hyperlink Forwarding System, you can show hyperlinks only when data exists at the destination. This is useful because users can know whether the link is active or not. If there is no data at the destination, "No Link" will be shown. Please see the HTML sources of the following two examples, and copy and paste them as you like (you need to change only IDs).
Sample 1
Sample 2
The sample 1 shows hyperlinks to Locus view of H-InvDB based on a OMIM ID. The sample 2 shows hyperlinks to 24 kinds of databases. By simply inserting several lines of JavaScript in your HTML, you can use this function.

3. All database search

By specifying IDs of any kind, this system searches for IDs in other databases that correspond to the specified IDs. By default, [All Databases] is selected as a database to open.
Highlighting newly linked data: Newly linked data since Monday in the previous week are highlighted with blinking "New" marks. So, if you open the All Database Search at least once in every week, you will not miss newly linked data.

Usage


    Search page

    (1)The form of converted ID is selected.
    ID/Type list

    (2)Input converted ID.

    (3)The data base of the forwarding destination is selected.
    Database list

    (4)Please click "Search".
    The search result will be displayed.


    Result page

4. ID converter system

- ID converter system

5. Downloading ID tables

You can download corresponding tables of two IDs. Select two IDs, push the search button, and start downloading the file of corresponding tables. The files are in tab-delimited text format.

6. ID Resolver

"ID Resolver" is a tool for discriminating various types of data IDs. If you have any data IDs of unknown origin, please try it. Multiple IDs can be discriminated at a time.

Usage

    (1)Input IDs (Figure 1)
    Input IDs of unknown origins. You can input multiple IDs separated by commas, spaces, or new lines.


    Figure 1. Input

    (2)Push the "Search" button
    Results (Figure 2) are shown in a table. From left to right, category of IDs, IDs (input), types of IDs, kinds of database (with links, Fig 2A), and links to "All Database Search" (icons) are shown. You can download the results by pushing the "Download" button above (Fig 2B). A tab-delimited file will be downloaded.


    Figure 2. Results

    Distinguishable IDs Please refer to the tables here.

7. Web Service

- Web service

8. Collected databases/IDs

This system acquires data from the following data bases.
We analyze correspondence of data IDs based on the following ID networks. By tracing the paths connected by solid lines, we make corresponding tables for all possible pairs of IDs.
database for for human

H-InvDB   http://www.h-invitational.jp/hinv/ahg-db/index.jsp

-Accession Number
-H-Inv transcript ID(HIT)
-H-Inv cluster ID (HIX)
-H-Inv protein ID (HIP)

NCBI   http://www.ncbi.nlm.nih.gov/

-Accession Number
-HUGO gene symbol
-RefSeq
-OMIM ID
-GeneID
-PubMed ID

HUGO   http://www.genenames.org/

-HUGO gene symbol
-RefSeq

H-GOLD   http://www.h-invitational.jp/gdbs/

-Accession Number
-H-GOLD Marker ID

GeMDBJ   https://gemdbj.nibio.go.jp/

-HUGO gene symbol
-dbSNP rs#

PDBj   http://www.pdbj.org/

-UniProt Accession Number
-PDB ID

MutationView   http://mutview.dmb.med.keio.ac.jp/MutationView/jsp/mutview/index.jsp

-HUGO gene symbol
-OMIM ID

Ensembl   http://www.ensembl.org/index.html

-HUGO gene symbol
-Ensembl Transcript ID (ENST)
-Ensembl Gene ID (ENSG)

UniProt   http://www.uniprot.org/

-UniProt Accession Number
-Accession Number

fRNAdb   http://www.ncrna.org/frnadb

-Accession Number
-fRNAdb ID

GGDB   http://riodb.ibase.aist.go.jp/rcmg/ggdb/

-HUGO Gene Symbol
-RefSeq

HGPD   http://www.HGPD.jp/

-Accession Number
-Clone ID
-FLJ ID

KEGG   http://www.genome.jp/kegg/

-GeneID
-KEGG Gene ID
-KEGG Pathway ID

HPRD   http://www.hprd.org/

-GeneID
-HPRD ID

NBRC   http://www.nbrc.nite.go.jp/e/index.html

-Accession Number
-Clone ID
-FLJ ID

LEGENA   http://h-invitational.jp/legenda/top.htm

-GeneID

Evola   http://www.h-invitational.jp/evola/search.html

-Mouse Accession Number
-H-Inv transcript ID(HIT)

H-DBAS   http://h-invitational.jp/h-dbas/

-Accession Number
-H-Inv cluster ID (HIX)

G-Compass   http://h-invitational.jp/g-compass/

-Accession Number
-H-Inv transcript ID(HIT)

Protein View   http://h-invitational.jp/hinv/help/help_index.html

-Accession Number
-H-Inv protein ID (HIP)

CIPRO   http://cipro.ibio.jp/

-Accession Number
-CIPRO ID

H-ANGEL   http://h-invitational.jp/hinv/h-angel/

-Accession Number
-H-Inv protein ID (HIP)

FLJ Human cDNA   http://flj.hinv.jp/

-Accession Number
-Clone ID
-FLJ ID

VarySysDB   http://h-invitational.jp/varygene/home.htm

-Accession Number
-H-Inv transcript ID(HIT)


Figure. ID network for human molecular data


database for mouse

NCBI   http://www.ncbi.nlm.nih.gov/

-Accession Number
-RefSeq
-GeneID
-PubMed ID

Ensembl   http://www.ensembl.org/index.html

-Accession Number
-Ensembl Transcript ID (ENST)
-Ensembl Gene ID (ENSG)

UniProt   http://www.uniprot.org/

-UniProt Accession Number
-Accession Number

KEGG   http://www.genome.jp/kegg/

-GeneID
-KEGG Gene ID
-KEGG Pathway ID

Evola   http://www.h-invitational.jp/evola/search.html

-H-Inv transcript ID(HIT)
-Accession Number

MGI   http://www.informatics.jax.org/

-MGI Marker Accession ID
-Accession Number
-Mouse Gene Symbol

IKMC   http://www.knockoutmouse.org

-MGI Marker Accession ID

FANTOM   http://fantom3.gsc.riken.jp/

-Accession Number
-Clone ID(FANTOM)

PDB   http://www.pdbj.org/

-PDB ID
-UniProt Accession Number

BRC Mouse Strain   https://database.riken.jp/sw/en/BRC_Mouse_Strain/cria315s1i/   

-BRC ID
-Allele ID
-MGI Marker Accession ID

MGI Allele   http://www.informatics.jax.org/

-Allele ID
-MGI Marker Accession ID




Figure. ID network for mouse molecular data


database for Chemical compounds

PubChem   http://pubchem.ncbi.nlm.nih.gov/

-PubChem Compound ID
-PubChem Substance ID
-ChEBI ID

DrugBank   http://www.drugbank.ca/

-DrugBank ID
-PubChem Compound ID
-Uniprot Accession Number

KeggDrug   http://www.kegg.jp/kegg/drug/

-KEGG Drug ID
-PubChem Substance ID

KeggCompound   http://www.genome.jp/kegg/compound/

-KEGG Compound ID
-PubChem Substance ID
-NIKKAJI ID

ChEBI   http://www.ebi.ac.uk/chebi/

-ChEBI ID
-PDBeChem ID
-PubMed ID
-CAS ID

PharmGKB   http://www.pharmgkb.org/

-PharmGKB IDr
-DrugBank ID

PDBeChem   http://www.ebi.ac.uk/msd-srv/msdchem/cgi-bin/cgi.pl?APPLICATION=1

-PDBeChem ID
-PDB ID

NIKKAJI   http://nikkajiweb.jst.go.jp/nikkaji_web/pages/top_e.jsp

-NIKKAJI ID

PDBj   http://www.pdbj.org/

-PDB ID

UniProt   http://www.pir.uniprot.org/

-Uniprot Accession Number
-Accession Number




Figure．ID network for chemical compounds and drugs.

For chemical compounds and drugs, we linked between IDs of the same molecules.
For UniProt protein sequences, we linked to "target proteins" that are known to bind with the chemicals and drugs in question.
For PDB structure data, we linked to structure data of protein complexes that contain the chemicals or drugs.


database for Ciona intestinalis

NCBI   http://www.ncbi.nlm.nih.gov/

-Accession Number
-RefSeq
-GeneID
-PubMed ID

UniProt   http://www.uniprot.org/

-UniProt Accession Number
-UniRef100 Accession Number
-Accession Number

Ensembl   http://www.ensembl.org/index.html

-Ensembl Transcript ID (ENST)
-Ensembl Gene ID (ENSG)

Cipro   http://cipro.ibio.jp/

-Cipro ID
-RefSeq
-H-Inv transcript ID(HIT)

Ghost   http://hoya.zool.kyoto-u.ac.jp/

-Ghost ID
-Cipro ID

Aniseed   http://aniseed-ibdm.univ-mrs.fr/index.php

-Aniseed Gene ID
-Cipro ID




Figure. ID network for Ciona intestinalis data


9. Release history

  • December 26, 2007 Official public release of Hyperlink Management System.
  • June 19, 2008 PDBj, MutationView were included. Official public release of ID Converter System.
  • January 06, 2009 Ensembl, GGDB and HPRD were included.
  • January 12, 2009 This system was licensed under a Creative Commons License.
  • August 20, 2009 "All Databases" was added as a target database of Hyperlink Management System.
  • September 29, 2009 KEGG were included.
  • October 21, 2009 HPRD were included.
  • December 28, 2009 "previous symbols" of HUGO Gene Symbol were added.
  • January 28, 2010 PubMed, GenBank, OMIM and NBRC were included.
  • February 25, 2010 Downloading data ID tables was enabled. LEGENDA and Evola were included.
  • April 08, 2010 For mouse,NCBI,Ensembl,Uniprot,KEGG,Evola,MGI and IKMC were added.
  • April 20, 2010 FANTOM were included.
  • May 26, 2010 H-DBAS, G-Compass, Protein View were included.
  • Jun 30, 2010 CIPRO, H-ANGEL, FLJ Human cDNA, VarySysDB were included.
  • September 10, 2010 We started a Pre-release of "Chemical comounds and Drugs". PubChem,DrugBank,KeggDrug,KeggCompound,ChEBI,PharmGKB and NIKKAJI were included.
  • December 14, 2010 "secondary accession number" of Uniprot were added.
  • January 27, 2011 "secondary accession number" of GenBank were added.
  • February 16, 2011 ID Resolver was enabled.
  • March 07, 2011 We started a Pre-release of "Ciona intestinalis". NCBI,Ensembl,Uniprot and Cipro were included.
  • April 13, 2011 We started an Official public release of "Ciona intestinalis". Ghost and aniseed were included.
  • May 10, 2011 Mouse Gene Symbol were included.
  • August 01, 2011 Wikipedia Human proteins were included.
  • September 14, 2011 JSNP DATABASE were included.
  • October 26, 2011 Mouse PDB, BRC Mouse Strain and MGI Alleles were included.
  • December 12, 2011 Newly linked data are highlighted in All Database Search.
  • February 7, 2012 We started an Official public release of "Rattus norvegicus". NCBI,Ensembl,Uniprot,Evola and RGD were included.
  • March 9, 2012 KEGG(Rattus norvegicus) were included.
  • April 6, 2012 KNApSAcK, JECDB and HMDB(Chemical compounds and Drugs) were included.